5IGK
Crystal structure of the first bromodomain of human BRD4 in complex with bromosporine (BSP)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2OSS | 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C |
experimental model | PDB | 2OUO | 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C |
experimental model | PDB | 2GRC | 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C |
experimental model | PDB | 2OO1 | 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C |
experimental model | PDB | 3DAI | 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C |
experimental model | PDB | 3D7C | 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 277 | 0.2 M Na/K(tart), 0.1 M BTProp pH 8.5, 20% PEG3350, 10% EtGly |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.24 | 45.07 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 39.465 | ¦Á = 90 |
b = 43.848 | ¦Â = 90 |
c = 78.016 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | IMAGE PLATE | RIGAKU | 2012-11-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E SUPERBRIGHT | 1.52 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | |||||||
1 | 1.7 | 19.5 | 97.1 | 0.043 | 0.022 | 21.1 | 4.7 | 15007 | 18.8 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.7 | 1.79 | 94.9 | 0.244 | 5.9 | 4.6 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C | 1.7 | 19.5 | 14222 | 749 | 96.71 | 0.15793 | 0.15583 | 0.19981 | RANDOM | 22.287 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.34 | 0.21 | -0.55 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.854 |
r_dihedral_angle_3_deg | 12.803 |
r_dihedral_angle_4_deg | 10.325 |
r_dihedral_angle_1_deg | 6.074 |
r_angle_refined_deg | 1.637 |
r_angle_other_deg | 0.882 |
r_chiral_restr | 0.094 |
r_bond_refined_d | 0.014 |
r_gen_planes_refined | 0.012 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1056 |
Nucleic Acid Atoms | |
Solvent Atoms | 118 |
Heterogen Atoms | 32 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
PHASER | phasing |